The Hybrid Child
by AgentMaryMargaretSkitz
Summary: A trip to the past for the Doctor, Clara, and their son does not go the way they hope. (Or Leopold Fitz is the son of the Twelfth Doctor and Clara)
1. Chapter 1

**So the story behind this is a gifset that had Twelve and Fitz side by side and giving a reason that Leo Fitz might be the son of the twelfth Doctor and Clara. Being trash for Twelve, Clara, Whouffaldi, and Fitz, I got sucked into this theory with a few others, and am bananas about it. I know I've written Leo as the Thirteenth Doctor before, but ugh this theory just seems to make sense to me. And I had to write something for it.**

 **So for sake of happiness, let's say the raven thing never happened.**

 **Hope you all enjoy! (This is my first time writing Whouffaldi in a fic. I tried. I don't get many prompts for them)**

* * *

"She's not doing anything," the little boy whined, peering in between the bars of the crib at the sleeping baby. "Mum, why isn't she doing anything?"

"Well, Leo, she's sleeping right now," Clara Oswald said to her son gently. "Babies do that a lot. You slept a lot too when you were that small. Sometimes you'd be with Daddy, and you would fall asleep right on top of him."

The five year old giggled, and Clara had to laugh too at the memory. Inside the crib, the little girl stirred and started to wake up. Clara picked Leo up, holding him against her hip so he could get a better glimpse at her. Her son grinned and waved down at her. In return, the baby gave him a gummy smile and gurgled.

"She's saying hello and that she likes you," the Doctor chuckled as he entered the room with the girl's father, who were now looking at him in puzzlement.

"He speaks baby," Clara explained, setting Leo back down and watching him run over to his father.

"Ah," the girl's father nodded while the baby gurgled some more.

"She's a bright girl, Dr. Johnson," murmured the Doctor, peering over in the crib. "Special too."

"You know her mother's gift. After all, you've met her a few times."

"Hm, fair point," the Time Lord mused before looking down at Leo. "What do you think, Leo? Do you want to stop by again someday and have a playdate with…sorry, what's her name again?"

"Daisy," Dr. Johnson said proudly, picking up his daughter as she started to fuss.

The Doctor's smile dropped a little, but he managed to hold it in place. "Daisy Johnson. That's…a lovely name."

Clara exchanged a worried glance with him, and he shot one back that meant they were going to have to talk later.

* * *

They should have left immediately when they found out the girl was Daisy Johnson. That part was something both the Doctor and Clara agreed on when they finally got back to the TARDIS and out of the mess. The previous night, when they'd stayed with the family at their insistence, they had discussed it at length while Leo slept. They had chosen to stay in an attempt to change history, to allow Daisy to grow up with a loving family and free from sadness that would befall her if they could prevent the tragedy. Daisy meant everything to her parents, just like Leo meant everything to them. If something terrible was coming to take him away from them, both the Doctor and Clara would have done everything in their power to stop the threat.

So they had stayed, and the following day they attempted to prevent the disaster that struck. Unfortunately, they were unable to stop it, despite their best efforts. Jiaying had been taken by Hydra, and Cal had gone after her while leaving Daisy behind with them. Then the massacre had begun, and they'd gotten their own son into the TARDIS before going back for Daisy. However, she was gone from they'd left her in her crib, and the body of the neighbor they'd had watch her was lying on the floor beside it. Seeing the corpse made them realize that they had failed.

The worst part was that Leo had seen too much. Their son had been on a few adventures before with them, but those ones were relatively tame and safe compared to the ones they had gone on before Clara found out she was pregnant. This time, there had been so many frightening things that no child his age should have had to see. He had seen Jiaying get kidnapped and had almost been taken as well.

Even worse, the family had run through the village during the massacre to get back to the TARDIS, and Clara had carried him the whole way, ordering Leo to close his eyes and not look at the spectacle. She'd hidden his face in her shoulder for good measure. He had run off to his room once they had gotten him inside. Now, even though the TARDIS confirmed he was onboard, their son was nowhere to be found.

"We should have just left," the Doctor lamented as they searched their son's room yet again. "He shouldn't have gone through all that."

"We can't change what happened," sighed Clara, getting up from where she'd been looking under Leo's bed. "He's not in here. Should we try the console room?"

The Doctor nodded, and they set off towards it. When they arrived, the Doctor looked around the lower level while Clara looked above.

"Leo?" she called, climbing the staircase up to the rows of bookshelves. "Leopold?"

A small sniffle came from her right by the Doctor's armchair. Clara approached it and sat down on the floor beside it. "Leo?"

The sniffling stopped as a small curly head poked out from behind the chair.

"Do you want to come out from behind there?" she asked gently.

Her son crawled out from the shadows and plopped down next to her. His eyes were red from crying.

"That was some scary stuff that we saw, huh?" she murmured as he leaned against her. "Mummy and Daddy didn't mean for you to have to go through all that."

Leo didn't say anything. He simply fidgeted a little beside her.

"You know, I was afraid we had left him behind," the Doctor chuckled as he came up the staircase. "We couldn't find you on the TARDIS anywhere."

Suddenly, Leo started to cry. He ran towards his father, flinging his arms around his legs while sobbing.

At the sight of his distraught son, the Doctor looked up at Clara, panicked. "What did I do?"

"Maybe the leaving him behind bit?" Clara huffed. "That's not something to joke about with a five year old, especially after what just happened."

"Oh, I didn't mean it like that!" the Doctor said, squatting down to sit on the top step and hugging his son properly. "I'd never do that to you, Leo. Always need to make sure all passengers are aboard the TARDIS, and you and Mum are top priority."

"S'not that," he whimpered, sitting down.

"So what is it?" Clara asked, moving close so that Leo was in between them. "Leo, you can tell us. We want to be able to help you."

"I don't wanna get taken."

Clara exchanged a look with the Doctor. Their son had just voiced one of their biggest fears. Clara had experienced more than one nightmare about someone taking her child away from her, whether it was the Daleks or UNIT or something else. She'd told the Doctor about them, and he had admitted having similar fears. Leopold was half of two races. Human and Gallifreyan. A hybrid. "You're afraid someone's going to take you away from us?"

Leo nodded. "They took Ms. Jiaying 'cause she was different. I'm different too. What if someone takes me?"

"Well, they won't," Clara insisted stubbornly, smoothing his curls down. "Mum and Dad will never let anyone take you away like that. Never ever."

"But what if they do?"

"They won't succeed," the Doctor told him. "We would never let anyone get away with it. Nothing will stop us. Not the Daleks, not the Cybermen, and not even time itself. I would call in every favor I could to get you back, even if it's from Missy. We will do anything and everything to get you back."

"Really?"

"Really, we would," Clara assured Leo as he turned toward her. "Because we love you, Leopold."

Leo wiped his eyes and a little smile came across his face. Clara pulled him onto her lap and hugged him, kissing the top of his head. She could feel the beat of his hearts against her hands. He then wriggled off and hugged his father.

"Can we ever see her again?" he asked the Doctor. "I really wanted to play with her."

"I think there's a possibility that it could happen, as long as Mum's okay with it."

* * *

The blue box appeared on the empty street corner, and the family of three exited out of it. Leo's face lit up at the sight of the playground across the street where a few children were playing.

"Where's Daisy?" Leo asked as they crossed the street.

The Doctor put on his sunglasses and pointed at one child playing by herself in a sandbox. "Right there."

Clara bent down beside Leo. "Remember, she might not be called Daisy, so ask her name first. Don't talk about the future, or anything that's not from Earth."

"Yes, Mum."

"He'll be fine, Clara," the Doctor huffed. "He's been on playdates before. Just make sure you have fun."

"Okay, Dad," Leo nodded, fidgeting a little. "Can I go play now?"

"Go on then," Clara urged. She straightened up and smiled as Leo took off across the grass toward the sandbox where Daisy was.

"Would you really call in a favor from Missy?" she asked the Doctor once their son was out of earshot. "I mean, remember when Leo was a baby and she kidnapped him?"

"She was babysitting," the Doctor countered as they found a nearby park bench and sat down together.

"She took him while he was with us!"

"Yeah, I had to reminder her that we would have needed to ask her first if we had wanted one in the first place."

"But would you call in a favor from her if we needed it to get Leo back?"

"I would," the Doctor replied, watching Leo sit down beside Daisy in the sandbox. "I would do anything to get him back, or you. Or both of you. I never thought I would have a family again, not after I lost everything in the Time War. I'm not going to let anything take you or Leo away from me now. This time, I'm going to hold tight to the things I love."

* * *

 **So there you are. My attempt at writing this theory which I love to death. There's actually another story on AO3 with this theory that's a lot cooler. The Stars of Leo. You should all check it out.**

 **Leave a review, tell me what you think?**


	2. Chapter 2

**I didn't expect that I would be posting more of this, but here I am! I got a wonderful prompt off of AO3, had some discussion with fellow Wastebasket buddies, and had a lot of fun writing this. So now there's a sequel! More family fun for this wonderful theory!**

 **And also Missy, because who doesn't love her?**

* * *

 **When Missy Came to "Babysit"**

"Helloooo?" Missy called out as she entered the TARDIS.

She'd come across it in an alleyway a few minutes ago. It had been too long since she had last crossed paths with her old friend. Seeing his blue box made her feel a bit nostalgic for all the fun that they'd had the last time they'd met, when they were on Skaro.

"I'm hooome!" she shouted when no response came.

Still no response. The console room seemed oddly quiet with the lack of the Doctor and whoever he had for a current companion. She wondered how long it had been since he'd last seen her. Was he still traveling with Clara? Or had she left him and he'd moved on?

Shrugging, Missy slid down the railing to explore the underside and the halls below. There was no harm in exploration at all. The Doctor explored things all the time. Besides, it had been too long since she'd last been in his TARDIS. He'd cleaned up a lot since then, and moved out of that grungy phase it had been in. It was much sleeker now, really.

As Missy made her way down one of the halls, she heard a peculiar sound coming from one of the rooms up ahead of her. She hadn't heard that sound in ages. Last time she had, it had been ages ago, in another body on Gallifrey. Intrigued, Missy followed the baby's whimpers to the room, which turned out to be a nursery. She managed to find a lamp in the hall light and switched it on. To the left of her was a crib holding a fussy baby boy.

"Well, you weren't around the last time I was here," she remarked, approaching the crib and peering inside.

The baby turned his head to look up at her, large blue eyes full of curiosity. He whimpered again.

"Yeah, definitely not your mum," Missy snorted. "And I'm not Daddy either if that's your next question."

The boy's lower lip began to quiver suddenly. Missy leaned in and picked the baby up.

"Don't you cry now," she told him, rocking him back and forth. "You're fine."

The action settled the baby, and he seemed to calm down. Shifting him slightly in her arms, she moved her hand to support him better. On her hand, she could feel two hearts beating.

"Someone's been busy then," she muttered, no longer wondering who the boy's father was. "So the Doctor's your dad, huh?"

The baby gurgled, and Missy chuckled. "Yep, that sounds like him. Or the last him I crossed paths with anyway. Who's your mum?"

There was an interesting sort of baby noise, almost like a giggle.

"She's just Mum to you, huh? Anyway, what are you called?"

More babbling.

"Leo. So he didn't name you after me. That's a shame. And I can't believe he and whoever your mum is left you all on your own. Good thing that Auntie Missy dropped by."

Holding the baby in one arm, Missy flipped open her vortex manipulator.

"How about we go have some fun somewhere while I look after you? What do you think about that? Want to stay in this solar system, or would you prefer another galaxy?"

Leo made a noncommittal grunt.

"Well, you seem to know what you want," Missy mumbled, a hint of sarcasm in her voice. "How about dinosaurs? They're quite fun. Especially the big sweet Tyrannosaurus Rex."

* * *

Leo did enjoy the dinosaurs. They'd seen a lot since they'd arrived, but it appeared he'd found a favorite.

"Ah!" he cried, waving his hands up at the brontosaurus.

"Yes, he's a big one, and not even an adult. I don't think you can get on his-no, her back."

"Ooo!" Leo tilted his head back to the sky and laughed.

Missy followed his gaze. There was something up in the sky, drawing closer and closer by the minute. It looked like a large spaceship. She snuck a peek at her vortex manipulator to check the date again. They'd gone back to Earth over sixty five million years ago.

So it wasn't a meteorite that took out the dinosaurs after all.

She was betting the Doctor was behind this. Maybe not the current one, but one of his past faces. A lot of history had been made because of that man.

"Okay then, little one. Time to say good-bye to the dinos."

Leo pouted a little as she picked him up from the grass. He turned in her arms and waved goodbye at the brontosaurus before Missy activated the vortex manipulator.

* * *

"The French Revolution. All you need to know about it is that it was a bunch of Frenchies bit-fighting and squabbling with each other. And right now, we're in a time when everyone's heads were getting loped off. Fun times it was. You know, I think your dad's visited this time period a time or two."

"Dada?"

"No, don't think he's around," Missy sighed with a shrug. "Not the version you know at least. A younger Doctor's probably roaming about somewhere, getting into trouble. Now, how about we go into the square and see if anything fun's going on."

* * *

Twenty minutes later, they had left France and the Reign of Terror behind them. Leo had started crying before the executions started. Missy had realized that maybe it wasn't the most appropriate place for a baby. Maybe she'd drop by again and try when he was older. But for now, it was time for a new destination.

And a lesson.

"Can you say Aunt Missy?"

"Issy."

"No, no, _Missy_."

"Issy!"

"Missy."

"Issy, Issy, Issy!" Leo chanted before dissolving into a fit of giggles.

Missy sighed, watching the lava flow ooze past them. "Well, you're trying. I'm starting to think your mum's human though."

Leo didn't respond. Instead, he started crawling toward the edge by the lava flow. Missy stepped forward and grabbed him before he could fall into it. Somehow, she doubted the Doctor would be very pleased if the little tyke got hurt while he was in her care.

"No, you don't want to touch that," Missy lectured to Leo as he started to fuss his disappointment. "Now, the volcano up there is going to go crazy in a minute. Do you want to stay and watch it? Or shall we go off somewhere else?"

Leo wanted to go somewhere else.

"Okay, that's fine. We'll miss out on a lovely boom though. I hope you get more fun when you're older."

* * *

The last destination was Leo's favorite. Turned out that he really loved monkeys.

She'd taken him to some place on Earth. It was sort of jungle and humid, and there were loads of monkeys scurrying about that were engaging in a variety of activities. Some were climbing trees, others were running about with some kind of fruit, and a few were grooming each other up in the trees.

Leo had immediately begun to squirm in her arms the moment they arrived and he laid eyes on the little creatures. Missy had put him down as he started to get fidgety, and he'd crawled over to some younger monkeys and their mum. Currently, he was engaging in some sort of game where he tossed a piece of fruit and one of the baby monkeys would bring it back to him. Every time it happened, Leo giggled and clapped his hands together in joy.

She was really good at this babysitting thing. She ought to volunteer her services more often.

A wheezing groan began to fill the air. Missy turned toward it to see a blue box slowly materializing a few feet from where she was sitting on a tree stump.

Seemed her stint of babysitting was over.

"Dada!" Leo crowed as he saw the box. "Mum!"

The doors to the TARDIS opened once the noise stopped. Clara Oswald stormed out a moment later, clad in a nightie and robe. The Doctor followed her a moment later, wearing a hoodie and those plaid pants he'd been wearing on Skaro. So they actually were there to stay, and hadn't been a frivolous thing he'd donned because he thought he was going to die.

"Where is my son?" Clara hissed, striding up to her. "I swear, if you have hurt him in any way, I will tear you apart and make sure you don't regenerate!"

Missy smiled, now knowing who Leo's mum was. "So you're Mum."

"Where is he?!"

"Mum, mum, mum!"

Clara whirled toward the chanting of the boy and sprinted over to where he sat in the glass. "Leopold!"

"Mum!" Leo repeated as Clara bent down and picked him up as the Doctor followed her.

"Oh, we were so worried about you," Clara sighed, kissing Leo's forehead.

"Dada!" Leo reached toward his father. "'nkeys!"

"Yes, there's a lot of monkeys around here, aren't there."

"I thought he'd like them," Missy interrupted. "Although I think he's enjoyed everything I took him too. I'm quite good at this babysitting thing."

Clara's head whipped toward her. "Babysitting?"

"Of course. What did you think I was doing with him?"

The brunette passed Leo to his father. "Hold him for a moment."

The Doctor nodded. Missy saw him smile as Leo slumped against his hoodie, now looking tired form the events.

Clara, on the other hand, was now walking back over to her. She didn't look too pleased.

"Babysitting? You bloody KIDNAPPED him!" Clara shrieked. "We were asleep! All of us, for once, were asleep! At least until I heard Leo fussing, but then he stopped. I thought he had gone back to sleep, and then I heard YOU! I saw you disappear with him before I could say anything, and we've been chasing that signal off the vortex manipulator all throughout space and time ever since you ran off with my son!"

"Oh, so you've seen where we went? I picked out some great destinations, don't you think?"

"How mental are you?! You took him to see the dinosaurs wiped out. And the French Revolution. No, no, specifically the Reign of Terror. What were you thinking? Why would you take a child there?"

"There were lots of other children there. Looked a bit like street urchins-"

"And a volcano. An active volcano that was about to have a massive eruption! The Doctor and I almost didn't get out of there in time before the lava hit us. This spot right here is the first appropriate place you've brought him too. And you call yourself a babysitter? You kidnapped him, you psychotic Mary Poppins!"

Clara took a step back, her rant finished. "Doctor, anything to add?"

"Think you covered it all," the Time Lord responded as he came over with Leo. "He's exhausted now. I'm sure he'll be out for a while."

"'nkey," the boy mumbled sleepily against his father.

"He wants a monkey now though."

Clara laughed. "Maybe when he's older. And no, Missy, you are not giving him one."

"Shame," she pouted. "I was thinking about getting him one for his birthday. When is it, by the way?"

The Doctor sighed and handed Leo back to Clara. "Get him back into his room. I'll be there in a moment."

Clara nodded and stood up on her tiptoes to kiss him. "Don't take too long."

Missy raised her eyebrows at them. Certainly they'd come a long way since she'd last seen them. Her matchmaking skills were just as good as her babysitting ones.

"Issy," Leo murmured softly, looking sleepily at her from over Clara's shoulder as the two went back to the TARDIS.

Missy smiled in their direction before turning back to the Doctor. "Just you and me now."

The Doctor narrows his eyes. "Never do anything like this again."

"What, babysit?"

"It was kidnapping, not babysitting!" he snapped. "And you endangered my son!"

"It's not like I took him to the first time the Black Plague was running amok on Earth. Or when Chen-7 was at its height Apalapucia."

The Doctor's expression didn't change.

"So have long have you had him?" Missy asked, hoping to change the subject slightly.

"He's seven months old," the Doctor replied, pride in his voice.

"Never got a birth announcement from you two."

"You weren't on the list," the Doctor said, turning around and walking back to the TARDIS.

Before he entered, her friend paused and turned back to her. "Don't come by again unless we need you. And if we do, we'll give you a ring."

"I don't think you have my number."

"Exactly."

With that, he disappeared into the TARDIS. It dematerialized seconds later, leaving Missy alone with the monkeys.

She turned and looked down at one of them. "I still think I did an excellent job looking after him."

* * *

 _2013_

"Agent Fitz?"

Leo Fitz turned around, almost dropping his mug when he saw who it was. "Director Fury? What are you doing here?"

"Came to find you. Something's come up and we need your assistance."

Leo checked to make sure they were alone. "Is this specific to my field, or is it alien-related?"

"The latter. Can you spare a moment?"

"Uh, sure."

Leo scribbled a quick note for Simmons to read when she got back from lunch before following the Director of SHIELD. He trailed behind Fury, his hearts thumping against his chest. Aside from Simmons, Fury was the only person at SHIELD that knew that he was half alien. Occasionally, he would get called in from time to time about certain alien anomalies that appeared on SHIELD's radar. Most of the time, he knew what they were. When he didn't, they usually handed it over to UNIT.

"So what's the situation?"

"We need you to identify someone," Fury explained, pressing the down button for the elevator. "We caught a woman trying to make off with some of the things we found in the streets after New York. She claims to know the Doctor, and she's not human."

"Does she look human?"

"On the outside, yes. But she's got two hearts, just like you."

An idea of the identity of the mystery person hit Leo as soon as he entered the elevator. "Does she look like a crazy Scottish Mary Poppins?"

Fury turned to him as the car began to descend. "That description hadn't occurred to me yet, but it seems fitting now."

Leo groaned. "I have a feeling I know who she is."

* * *

 **And there we go! Another addition in this beautiful universe, and another fanfic for the Wastebasket.**

 **Leave a review, tell me what you think! And if you have any ideas/headcanons, feel free to drop them off. I'll flip out over anything really.**


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